From the green chlorophyll in plants and algae that we depend upon to transform sunlight into useful energy, to the red heme that carries oxygen to the cells in our bodies, porphyrins are the colors of life. It is not surprising then, that porphyrins have been actively interrogated as tools for diverse applications to improve biotechnology and medicine. With the goal of improving cancer therapy and diagnosis in mind, this thesis examines new modular porphyrin architectures. These constructs have interesting properties that extend beyond their originally intended use as phototherapeutic agents. In Chapter 1, a comprehensive background on porphyrin-based activatable photosensitizers is presented. In Chapter 2, porphyrin singlet oxygen and fluorescence quenching is examined in a model system with respect to Förster theory. Chapter 3 examines a new DNA responsive molecular beacon that was quenched using multiple quenching moieties and its application for nanoparticle aggregation. Chapter 4 describes extremely self-quenched nanovesicles formed from porphyrin-lipid conjugates that displayed a number of desirable properties for nanomedicine applications. Chapter 5 presents a brief discussion and some potential future directions of the research. It is my hope that the data presented in this thesis set the stage for new porphyrin-based approaches to make a translational impact in the battle against cancer and other diseases.

Degeneration of the intervertebral discs is the most common cause of back pain. The early stages of degeneration affect the nucleus pulposus (NP) of the intervertebral discs followed by a rapid degeneration of the annulus fibrosus. Regeneration of the NP may slow down or reverse the progression of the disease. A new deacetylated derivative of a marine diatomic glycosaminoglycan was developed to obtain a hydrogel formulation proposed to have a reparative effect on damaged NP tissue. The hydration kinetics and viscoelastic behaviour of the hydrogel under shear were studied and compared with the behaviour of nondegenerated human lumbar NP. In vitro studies were conducted using primary cell cultures treated with the drug to study cell viability and extracellular matrix factor expression. In vivo studies using New Zealand White (NZW) rabbits have also been conducted using MRI to quantify disc volume followed by histological and immunohistochemical analysis. Rheological data has indicated that the elastic component of the hydrogel dominates the viscous component over a frequency range of 0.1 to 15.85 rad/s. Proteoglycan expression of the treated cells was found to be 78.4 ± 1.9 (p<0.05) times higher than the untreated controls. RTPCR and immunohistochemical data from in vitro studies have demonstrated that characteristic the chondrocyte markers, aggrecan and collagen II, are expressed in the treated cells. A comparison of disc volumes at 6 weeks post-op has shown that the treated discs have 41% greater volume than the untreated iii discs (p<0.05). The results obtained in this study demonstrate that the sulfated deacetylated glycosaminoglycan derivative is a promising material to be utilized in treatment of NP degeneration.

Background: Computerized Provider Order Entry (CPOE) allows providers to enter medication and service orders electronically. Workflow analysis is a critical component of CPOE implementation. Objectives 1. To develop a nosology for provider ordering workflow. 2. To describe actual provider ordering workflow focusing on chart and computer usage 3. To model the impact of computerized ordering on provider workflow in three future state scenarios Method: 20 hours of participant observation was performed for nosology development, time motion studies totaling 47 and predictive modeling projected effects of possible implementation scenarios Results/Conclusions: Unique nosology was developed. Clinicians spent 27% of their time with the patient, 2.2% writing orders and 1.1% locating patient charts. Our study predicted that the E-All scenario (computerization of all orders) would be the best implementation choice. Limitations: Small sample size (25 clinicians), participant frame of reference and other assumptions may have affected the results of this study.

Topographical orientation is the ability to orient oneself within the environment and to navigate through it to specific destinations. Topographical disorientation (TD) refers to deficits in orientation and navigation in the real environment, and is a common sequela of brain injuries. People with TD often have difficulties interacting with and perceiving the surrounding environment. The literature suggests that patients with TD are likely to benefit from research leading to clinical standards of practice and technology to facilitate topographical orientation. In the light of the above, the objectives of this thesis were to investigate methods of realizing a context-aware, wearable mediated environment system for indoor navigation, and to develop a standard method of quantifying the impact of such a system on indoor navigation task performance. In realizing these objectives, we first conducted an extensive literature review of in-door localization systems. This review served to identify potential technologies for an indoor, in-situ wayfinding assistive device. Subsequently, an automated navigation algorithm was designed. Our algorithm reduced the navigational effort of simulated patients with topographical disorientation while accounting for the physical abilities of the patient, environmental barriers and dynamic building changes. We introduced and demonstrated a novel energy-based wayfinding metric, which is independent of route complexity. An experiment was conducted to identify preferred graphical navigation tools for mediated reality wayfinding guidance. Different combinations of spatial knowledge, graphical presentations and reference frames were considered in the experiment. The data suggested that the locator and minimap are the preferred navigational tools. Two unique optical-inertial localization systems for real-time indoor human tracking were created. The first localization system was oriented to pedestrians, while the second was implemented on a wheelchair. Empirical tests produced localization accuracies comparable to those reported in literature. Finally, a fully operational mediated reality location aware system for indoor navigation was realized. Tests with human participants indicated a significant reduction in physical effort in comparison to the no-tool condition, during wayfinding tasks in an unfamiliar indoor environment. Collectively, the findings and developments of this thesis lay the foundation for future research on wearable, location-based navigational assistance for individuals with wayfinding difficulties.

When routine repair mechanisms fail to regenerate severe burn wounds, mesenchymal stem cell therapy is considered. However, engrafted mesenchymal stem cells are prone to become myofibroblasts when exposed to high mechanical tension and pro-fibrotic cytokines in the wound microenvironment. Myofibroblast activity increases wound stiffness and activates healthy precursor cells into destructive phenotype, resulting in pathological remodelling and hypertrophic scarring. Using soft silicone substrates with near-physiological stiffness, I tested the hypothesis that myofibroblast characteristics acquired by mesenchymal stem cells in cell culture are preserved by microRNA modifications typical for fibrosis and demonstrated that priming mesenchymal stem cells on soft substrates protect them from subsequent activation and that the mechanically propagated myofibroblast memory is mediated by miR-21. This study aims to demonstrate that suppressing myofibroblast activation will maximize and prolong the beneficial regenerative effects of mesenchymal stem cells while terminating harmful and excessive tissue remodelling characteristic for fibrosis upon engraftment.

When routine repair mechanisms fail to regenerate severe burn wounds, mesenchymal stem cell therapy is considered. However, engrafted mesenchymal stem cells are prone to become myofibroblasts when exposed to high mechanical tension and pro-fibrotic cytokines in the wound microenvironment. Myofibroblast activity increases wound stiffness and activates healthy precursor cells into destructive phenotype, resulting in pathological remodelling and hypertrophic scarring. Using soft silicone substrates with near-physiological stiffness, I tested the hypothesis that myofibroblast characteristics acquired by mesenchymal stem cells in cell culture are preserved by microRNA modifications typical for fibrosis and demonstrated that priming mesenchymal stem cells on soft substrates protect them from subsequent activation and that the mechanically propagated myofibroblast memory is mediated by miR-21. This study aims to demonstrate that suppressing myofibroblast activation will maximize and prolong the beneficial regenerative effects of mesenchymal stem cells while terminating harmful and excessive tissue remodelling characteristic for fibrosis upon engraftment.

The freshwater zebra mussel Dreissena polymorpha is a biofouling species that adheres to varied substrates underwater using a proteinaceous byssus that consists of a bundle of threads tipped with adhesive plaques. This underwater adhesion is an inspiration for the development of medical and dental bioadhesives, however, the byssus is highly resistant to biochemical characterization owing to extensive cross-linking and therefore, limited information is available on the mechanisms of adhesion and cohesion of byssal proteins. We report here on the identification and sequence analysis of eight novel byssal proteins identified in the soluble extract and insoluble matrix from induced, freshly secreted byssal threads with minimal cross-linking, using gel electrophoresis and LC-MS/MS sequencing techniques. Identified byssal proteins have theoretical molecular weights ranging from 4.1 kDa to 20.1 kDa and isoelectric points ranging from 4.2 to 9.6 and have several common characteristics including consensus repeat patterns, block structures and defined sequence motifs.

The freshwater zebra mussel Dreissena polymorpha is a biofouling species that adheres to varied substrates underwater using a proteinaceous byssus that consists of a bundle of threads tipped with adhesive plaques. This underwater adhesion is an inspiration for the development of medical and dental bioadhesives, however, the byssus is highly resistant to biochemical characterization owing to extensive cross-linking and therefore, limited information is available on the mechanisms of adhesion and cohesion of byssal proteins. We report here on the identification and sequence analysis of eight novel byssal proteins identified in the soluble extract and insoluble matrix from induced, freshly secreted byssal threads with minimal cross-linking, using gel electrophoresis and LC-MS/MS sequencing techniques. Identified byssal proteins have theoretical molecular weights ranging from 4.1 kDa to 20.1 kDa and isoelectric points ranging from 4.2 to 9.6 and have several common characteristics including consensus repeat patterns, block structures and defined sequence motifs.

Despite the importance of inter-cellular (between cell) communication networks in regulating homeostasis in multicellular organisms, very little is known about their topology, dynamics, or functional significance. Inter-cellular communication networks are particularly relevant in stem cell biology, as stem cell fate decisions (self-renewal, proliferation, lineage specification) are tightly regulated based on physiological demand. Using human blood stem cell cultures as an experimental paradigm, we present an integrated experimental and computational approach to interrogate a hierarchically organized tissue network. We have developed a novel mathematical model of blood stem cell development incorporating cell-level kinetic parameters as functions of secreted molecule-mediated inter-cellular networks. By relation to quantitative cellular assays, our model is capable of predictively simulating many disparate features of both normal and malignant hematopoiesis, relating internal parameters and microenvironmental variables to measurable cell fate outcomes. Through integrated in silico and experimental analyses we show blood stem and progenitor cell fate is regulated by cell-cell feedback, and can be controlled non-cell autonomously by dynamically perturbing inter-cellular signalling. Furthermore, we have compiled genome-scale molecular profiles (transcriptome and secretome), publicly available databases, and literature mining to reconstruct soluble factor-mediated inter-cellular signalling networks regulating cell fate decisions. We find that dynamic interactions between positive and negative regulators, in the context of tuneable cell culture parameters, tip the balance between stem cell supportive vs. non-supportive conditions. The cell-cytokine interactions can be summarized as an antagonistic positive-negative feedback circuit wherein stem cell self-renewal is regulated by a balance of megakaryocyte-derived stimulatory factors vs. monocyte-derived inhibitory factors. To understand how the experimentally identified positive and negative regulatory signals are integrated at the intra-cellular level, we define a literature-derived blood stem cell self-renewal network wherein these extracellular signals converge for coherent processing into cell fate decisions. In summary, this work demonstrates the utility of integrating experimental and computational methods to explore complex cellular systems, and represents the first attempt to comprehensively elucidate non-autonomous signals balancing stem cell homeostasis and regeneration.

Communication disorders affect one in ten Canadians and the incidence is particularly high among those with Cerebral Palsy. A vocalization-activated switch is often explored as an alternative means to communication. However, most commercial speech recognition tools to date have limited capability to accommodate dysarthric speech and thus are often prematurely abandoned. We developed and evaluated a novel vocalization-based access technology as a writing tool for a pediatric participant with cerebral palsy. It consists of a high quality condenser headmic, a custom classifier based on Gaussian Mixture Modeling (GMM) and Mel-frequency Cepstral Coefficients (MFCC) as features. The system was designed to discriminate among five vowel sounds while interfaced to an on-screen keyboard. We used response efficiency theory to assess this technology in terms of goal attainment and satisfaction. The participant’s primary goal to reduce switch activation time was achieved with increased satisfaction and lower physical effort when compared to her previous pathway.